Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic variability parameters were found between individual populations. Private alleles have been identified in five out of six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis, and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises, which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we recommend focusing on the two populations with significant genetic distinctions from the others.

The potential of frozen rumen fluid for ruminant feed evaluation using in vitro gas production technique

The aim of this study was to determine the potential of frozen rumen fluid (RF) for ruminant feed evaluation using in vitro gas production (IVGP) technique. This study used a factorial randomized block design with a 3 × 3 × 3 pattern, consisting three feeding regimes varying in forage to concentrate proportion, namely 20%:80% (feed A), 40%:60% (feed B), and 60%:40% (feed C), respectively; three storage time (2, 11, and 19 days); and RF from 3 breeds of indigenous cattle, namely Bali, crossbred Ongole and Madura cattle as groups. The results showed that the effects of feeding regimes, inoculum source, or storage time on total gas production, potential of gas production, rate of gas production, dry matter and organic matter degradability. Based on the results, it can be concluded that frozen RF may be used as inoculum source for feed evaluation using the IVGP technique and hence it supports the previous findings reported in the literature. Considering that the effects of different feeds, inoculum sources, and storage times gave the specific values, it is advisable that to use RF from slaughtered animals should be taken from the same breed to allow accurate comparison for feed evaluation using IVGP technique.

Changes in microbiological parameters, pH and titratable acidity during the refrigerated and room temperature storage of dahi prepared from the milk of Vechur cows: an indigenous cattle breed of Kerala

Vechur cow is an indigenous cattle breed of Kerala listed as a critical breed by FAO. This research communication is related to the hypothesis that the changes occurring in microbiological quality parameters of Vechur cow milk dahi (VCMD) during storage will be superior to other milk and reflective of the traditional concepts of therapeutic properties attributed to Vechur milk. Microbiological quality of the VCMD stored at room (30 ± 1°C) and refrigerated (4 ± 1°C) temperatures in terms of total viable, coliform, yeast and mold and lactococcal counts is reported in this study, together with titratable acidity and pH. Results are compared with cross-bred cow milk dahi (CCMD) as control. On refrigerated storage, despite the comparable initial microbiological quality, VCMD exhibited significantly lower total viable, lactic acid bacteria, yeast and mold counts than CCMD, from the fifth day onwards for the first two parameters and the tenth day onwards for the last parameter. VCMD exhibited significantly higher pH values than CCMD from the fifth day onwards whereas the titratable acidity was significantly lower from the tenth day onwards. Though this study does not delineate the factors contributing towards the lower microbial population observed in VCMD, it provides an impetus to further researches for scientifically validating its traditionally-reported medicinal properties.

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

Microbiome Analysis Exploring Taxonomic Diversity in Kasaragod Dwarf and Holstein Crossbred Cattle

The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf cattle, a unique non-descriptive native cattle of Kerala, India, are noted for their unique qualities, such as low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. However, owing to the higher milk yield, Holstein crossbred cattle are given more importance over Kasaragod Dwarf. The hindgut microbiota plays a major role in various biological processes such as the digestion, vitamins synthesis, and immunity in cattle. In this study, we compared the hindgut microbiota of the Kasaragod Dwarf with the highly found, Holstein crossbred utilizing 16S rRNA high-throughput sequencing for a better understanding of the relationship between the host and microbial community. Four replicates of each 20 samples comprising two cattle type (n=10) were sequenced and analyzed. Marker gene-based taxonomic analysis affirmed variations in their microbial composition. Principle Coordinate Analysis (PCoA) using weighted and unweighted UniFrac distance matrices showed the distinct microbial architecture of the two cattle type. Random Forest analysis further confirmed the distinctness and revealed the signature taxa in K-Dwarf. The study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in Kasaragod Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in Kasaragod Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of Kasaragod Dwarf cattle gut microbiome profiling. This study is pivotal towards developing genetic resources for the microbial population in K-Dwarf and how it could be differentiated from Holstein crossbred cattle.

Varimax Rotated Principal Component Analysis of Productive Traits in Nigeria Indigenous Cattle Raised under Semi-Intensive Management System

The objectives of this study were to quantify the production traits using principal component analysis in Bunaji and Gudali cattle. Morphological traits of Body weight (Kg); BL: Body Length (Cm); HW: Height at withers (cm); CW: Chest width (cm); HG: Heart Girth (cm); Rumwi: Rump width (cm); TL: Teat Length (cm); RUH: Rear Udder Height (cm); UC: Udder Circumference (cm) and lactation traits of TY: Total Yield (Litres); ADY: Average Daily Yield (Litres/day) and LL: Lactation Length (days) were measured. To find the traits that were clustered together, data were fed to the principal component matrix of J.M.P genomics statistical software. In general, communalities varied from 0.32 to 0.91, and the proportion of variance accounted for by variables was 48 percent Bunaji, 0.31 to 0.99 for communalities, and 58 percent in Gudali cows. The information on principal component analysis will facilitate their efficient use in breeding programs for genetic gain and genetic improvement programs in indigenous Nigeria cattle.

Genetic Diversity of Nepalese Indigenous Cattle Breeds Based on D-Loop Mitochondrial DNA

Nepalese cattle are known for their genetic potentiality concerning inhabitant in extreme climatic conditions, surviving in the scarce food supply, and resistant to several diseases. We aimed to assess Nepal’s ancestral origin and genetic diversity of indigenous cattle breeds based on hyper-variable D loop mtDNA sequences. Three cattle breeds (Siri, Achammi, & Lulu) comprising the total sample population (n= 75) were employed in the study where the mt DNA information of two breeds (Achammi & Lulu) were retrieved from the published source. Hyper-variable D loop (910bp) of Siri cattle was PCR amplified and sequenced. This study claims that the possible ancestral origin of Bos taurus and Bos indicus mtDNA lineage in the Nepalese cattle population is majorly influenced by China and India, respectively. This study suggests that Nepalese cattle can be divided into two major groups: Bos taurus and Bos indicus, where most of the cattle population was of Bos indicus origin. The sampled population can be classified into three significant haplogroups: T3 (25%), I1 (48%), and I2 (27%) revealing a higher genetic diversity among the Nepalese cattle population. Only T3 taurine haplogroup was found in the sampled population. It was consistent with the fact that the absence of T1 haplogroup in North-East Asian cattle. In terms of Bos indicus, the I1 haplogroup was dominant over I2. Higher genetic diversity can be appropriate reasoning for Nepalese cattle’s survival in a harsh environment and low food conditions.

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning

Dianzhong cattle is a classic Chinese indigenous cattle breed with historical records dating back to 200 BC. But with its genomic differences having not been clearly elucidated, the quest for genomic characterization will be an essential step towards understanding the genomic basis of productivity and adaptation to survival under Chinese farming systems. Here we compared 10 Dianzhong cattle (four newly sequenced and six downloaded) with 29 published genomes of three underlying ancestral populations (Chinese zebu, Indian zebu, and Yanbian cattle) to characterize the genomic variations of Dianzhong cattle. Dianzhong cattle has a high nucleotide diversity (0.0034), second only to Chinese zebu. Together with analyses of linkage disequilibrium decay and runs of homozygosity, Dianzhong cattle displayed higher genomic diversity and weaker artificial selection compared with Yanbian cattle. From a selective sweep analysis by four methods (Fst, π-ratio, XP-CLR, and XP-EHH), the positive selective signals were mainly manifested in candidate genes and pathways related to heat resistance, growth and development, fat deposition, and male reproduction. Missense mutations were detected in candidate genes, SDS (c.944C > A and p.Ala315Glu), PDGFD (c.473A > G and p.Lys158Arg), and DDX4 (rs460251486, rs722912933, and rs517668236), which related to heat resistance, fat deposition, and spermatogenesis, respectively. Our findings unravel, at the genome-wide level, the unique diversity of Dianzhong cattle while emphasizing the opportunities for improvement of livestock productivity in further breeding programs.